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- PDB-3zj4: Neurospora Crassa Catalase-3 expressed in E. coli, triclinic form. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zj4 | ||||||
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Title | Neurospora Crassa Catalase-3 expressed in E. coli, triclinic form. | ||||||
![]() | CATALASE-3 | ||||||
![]() | OXIDOREDUCTASE / HYDROGEN PEROXIDE / PEROXIDASE | ||||||
Function / homology | ![]() catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zarate-Romero, A. / Rudino-Pinera, E. | ||||||
![]() | ![]() Title: Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3 Authors: Zarate-Romero, A. / Stojanoff, V. / Rojas-Trejo, S.P. / Hansberg, W. / Rudino-Pinera, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 532.2 KB | Display | ![]() |
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PDB format | ![]() | 436.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 91.8 KB | Display | |
Data in CIF | ![]() | 121.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zj5C ![]() 4bimC ![]() 3ej6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 82552.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: BEFORE RESIDUE 1 A HIS TAG SIGNATURE IS PRESENT / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100MM HEPES PH 7.5, 20 PERCENT PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2010 Details: SI(111) CHANNEL CUT MONOCHROMATOR, TOROIDAL FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→29.5 Å / Num. obs: 47857 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.66 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.1→3.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EJ6 Resolution: 3.098→29.399 Å / SU ML: 0.36 / σ(F): 1.96 / Phase error: 24.05 / Stereochemistry target values: ML Details: RESIDUES 37 TO 716 ARE VISIBLE IN THE ELECTRON DENSITY MAP. NCS WERE USED UNTIL THE LAST STEP OF THE REFINEMENT IN WHICH AFTER A NORMALISATION OF THE COORDINATES A RIGID BODY REFINEMENT WERE USED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.098→29.399 Å
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Refine LS restraints |
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LS refinement shell |
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